Method and compositions for immunization with the Pseudomonas V antigen

ABSTRACT

A method of inhibiting, moderating or diagnosing  Pseudomonas aeruginosa  infection is disclosed. In one embodiment, this method comprises inoculating a patient with an effective amount of PcrV antigen.

CROSS-REFERENCE TO RELATED APPLICATION

The present application is a continuation of U.S. patent application Ser. No. 10/496,059, filed Nov. 11, 2004 and issued as U.S. Pat. No. 7,494,653 on Feb. 24, 2009, which is a 371 of PCT/US02/02382, filed Jan. 25, 2002 and claims priority of U.S. patent application Ser. No. 09/770,916, filed Jan. 26, 2001 and issued as U.S. Pat. No. 6,827,935 on Dec. 7, 2004, and U.S. provisional patent application 60/264,795, filed Jan. 29, 2001. These documents are incorporated by reference herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with United States government support awarded by the following agencies: NIH/NIADA Grant Nos. R01 A131665-08, K04 A101289-04 and R01 HL59239-02. The United States has certain rights in this invention.

BACKGROUND OF THE INVENTION

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that is capable of causing fatal acute lung infections in critically ill individuals (1). The ability of the bacterium to damage the lung epithelium has been linked with the expression of toxins that are directly injected into eukaryotic cells via a type III-mediated secretion and translocation mechanism (2,3).

The proteins encoded by the P. aeruginosa type III secretion and translocation apparatus demonstrate a high level of amino acid identity with members of the Yersinia Yop regulon (4-6). Of all the type III systems discovered in Gram-negative bacteria, only P. aeruginosa possesses a homologue to the Yersinia V antigen, PcrV (see 6 for review of type III systems). Homologous proteins to the secretion and translocation apparatus are encoded by both plant and animal pathogenic bacteria. These organisms include human pathogens such as Salmonella typhimurium, Shigella flexneri, Enteropathogenic E. coli, Chlamydia spp., and plant pathogens such as Xanthamonas campestris, Pseudomonas syringe, Erwinia amylovora and Ralstonia solanacearum. However, only P. aeruginosa and Yersinia encode the V antigen.

Yahr, et al., 1997, discloses the sequence of the operon encoding PcrV and compares the sequence to the LcrV protein. Thus, the nucleic acid sequence of PcrV is known and is available under accession number AF010149 of GenBank (SEQ ID NO:8).

DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B are a stained gel (FIG. 1A) and Western blot (FIG. 1B) illustrating the phenotypic analysis of PA103ApcrV.

FIGS. 2A and 2B are a graph (FIG. 2A) and set of bar graphs (FIG. 2B) illustrating the survival and lung injury of P. aeruginosa parental and mutant strains.

FIGS. 3A and 3B are a graph (FIG. 3A) and a set of bar graphs (FIG. 3B) illustrating the effect of immunization on survival, lung injury, and bacterial colonization.

FIG. 4 is a graph of the number of animals surviving a challenge with 5×10⁵ CFU/mouse of strain PA103 after passive administration of polyclonal IgG specific for PcrV, ExoU, PopD or control IgG from an unimmunized animal.

FIG. 5 is a graph (FIG. 5A) and a set of bar graphs (FIG. 5B) illustrating survival and protection from lung injury by concomitant administration of IgG to different bacterial antigens and bacterial challenge. One-way ANOVA for lung injury, p=0.026, and lung edema, p<0.0005.

FIGS. 6A and B are printouts of SEQ ID NOs:1 and 2 with additional explanatory information. FIG. 6A is SEQ ID NO:1. FIG. 6B is SEQ ID NO:2.

FIG. 7 is a printout of SEQ ID NOs:3 and 4 with additional explanatory information.

FIG. 8 is a synthetic recombinant single chain antibody (SCFV-M166) (SEQ ID NOs:5 and 6).

SUMMARY OF THE INVENTION

The present invention involves methods and compositions developed from our observation that the Pseudomonas V antigen can be used to protect animals from a lethal lung infection.

In one embodiment, the present invention is a method of inhibiting Pseudomonas infection comprising inoculating a patient with an effective amount of PcrV antigen. In another embodiment, DNA encoding PcrV is used as a gene vaccine.

In one preferred embodiment, the antigen is expressed as a recombinant protein and used to immunize patients at risk.

Preferably, the patient is completely protected from infection.

In another embodiment, the DNA encoding PcrV (called pcrv) or a DNA fragment may be used diagnostically to detect P. aeruginosa infection.

In another embodiment, the recombinant protein (rPcrV) is used diagnostically to detect antibodies from patients. Patient antibody response to PcrV may be associated with prognosis. Therefore, in this embodiment the recombinant protein is used as a prognostic indicator by measuring the patient's antibody titer.

The present invention also provides a method for inhibiting a Pseudomonas infection in an individual by contacting the individual with an effective amount of a PcrV inhibitor, in particular with a PcrV antibody, antibody derivative or fragment, or antibody mimic. PcrV antibodies, antibody derivatives and antibody fragments are also provided.

It is an object of the present invention to actively and passively immunize a patient against Pseudomonas infection.

It is another object of the present invention to diagnostically detect the P. aeruginosa infection.

It is another object of the present invention to diagnostically detect antibodies from Pseudomonas patients.

Other objects, features and advantages of the present invention will become apparent to one of skill in the art after review of the specification, claims and drawings.

DESCRIPTION OF THE INVENTION

We disclose herein that PcrV has a novel regulatory effect on expression of the type III secreted products, is involved in the translocation of type III toxins, and is the first antigen that protects against lung injury induced by P. aeruginosa infection. Vaccination against PcrV prior to the airspace instillation of anti-PcrV IgG not only ensured the survival of challenged animals but also decreased lung inflammation and injury caused by the bacteria.

LcrV, or the V antigen, is a multifunctional protein that regulates secretion/translocation of the Yop effector proteins and plays an extracellular role in pathogenesis by altering the host cytokine response to Yersinia infection (7-11). The only known homologue of this critical pathogenic factor is an extracellular protein encoded by P. aeruginosa, termed PcrV.

One embodiment of the present invention is a method of moderating or inhibiting a Pseudomonas infection by immunizing a patient with an effective amount of the PcrV antigen. By “effective amount” we mean an amount of PcrV antigen effective to show some moderation or inhibition of Pseudomonas infection as compared to control subjects or animals who have not been treated with the antigen.

By “moderating” we mean that infection is inhibited by at least fifty percent compared to a non-immunized animal. Preferably, infection is completely prevented. A quantitative assessment of infection would preferably include the examination of the amount of bacteria in the bloodstream or pleural fluids and/or an examination of lung injury parameters. For example, the absence of bacteria in the bloodstream or pleural fluids would indicate prevention of infection. A reduction in lung injury parameters would indicate that infection is moderated.

Infection could be quantitatively assessed by several other clinical indicators, including the reduction of bacterial load in the sputum, blood or pleural fluids, reduction in the size of the infiltrate, oxygenation improvement, reduction in the length of time on mechanical ventilation, reduction in fever and reduction in white blood cell count.

By “PcrV antigen” we mean that portion or fragment of the PcrV protein that is necessary to invoke an immune response which prevents or moderates infection. We have used the full-length PcrV protein as an antigen to induce protection. Additionally, we have mapped the protective epitope to the fragment comprising amino acids 144-257 of PcrV (SEQ ID NO:7). To define the epitope, monoclonal antibodies that protected against infection and cytotoxicity were tested for binding to progressively smaller forms of recombinant PcrV. (By “recombinant PcrV” or “rPcrV” we mean the protein produced from a PcrV gene that has been placed in a non-native host.) This protection localized the region.

The PcrV antigen may be most easily obtained by the method we used, commercially available bacterial expression plasmid pet16b from Novagen. The pcrV gene was first cloned from the P. aeruginosa chromosome as part of an operon. The coding region was amplified and inserted into two different vectors. One vector is for expression from P. aeruginosa as shown in FIG. 1. This is a vector from Herbert Schweizer (reference 19) which we modified to contain an appropriate promoter sequence such that PcrV expression is coordinately regulated with the rest of the delivery and intoxication apparatus of the bacterium. The second plasmid, pET16b, is for expression and purification purposes from E. coli.

The advantage of this system is that we do not have to worry about contaminating P. aeruginosa proteins, the protein is produced in great abundance, and there is a one-step purification process. In this situation the PcrV coding region is amplified to be cloned in frame with a histidine tag provided on the pET16b vector. The multiple histidine residues fused to the amino terminus of PcrV allow affinity chromatography using a nickel-NTA column. Therefore, a preferable PcrV antigen is a recombinant version of the natural PcrV protein.

Immunization may be done systemically or intranasally. Immunization of these individuals would preferably start during normal vaccination procedures for other childhood diseases. We would predict long-lived protection with booster doses probably around ages 5 and 10.

In another embodiment, one would use DNA encoding the PcrV protein or the complement of this DNA to diagnostically detect P. aeruginosa infection. One would obtain the DNA sequence of the PcrV antigen at GenBank AF010149. The coding region for PcrV is at nucleotides 626-1510. One may also choose to use a fragment of this coding region or complement of this fragment. A successful probe is one that will hybridize specifically to the PcrV DNA and not to other regions.

One would preferably use a hybridization probe of at least 40 continuous nucleotides within the antigen sequence or two primers of at least 25 continuous nucleotides within the sequence. One skilled in the art would appreciate that many standard forms of nucleic acid diagnostic techniques would be suitable, for example, hybridization of the single-stranded 40 nucleotide probe to DNA or RNA extracted from a patient's sputum. In another example, patient's sputum would be used as a source for bacterial DNA or RNA to serve as a template for the PCR or RT-PCR reaction, respectively.

One would also determine Pseudomonas aeruginosa infection in an individual by contacting a sample obtained from the individual with an antibody specific for PcrV and correlating enhanced antibody binding as compared with a control sample with Pseudomonas aeruginosa infection in the individual.

In an additional embodiment, the DNA encoding PcrV is used as a gene vaccine using standard molecular biological methods. For example, one could review the following references for techniques known to those of skill in the art: Davis, H. L., et al., “DNA vaccine for hepatitis B: Evidence for immunogenicity in chimpanzees and comparison with other vaccines,” Proc. Natl. Acad. Sci. 93:7213-7218, 1996; Barry, M. A., et al., “Protection against mycoplasma infection using expression-library immunization,” Nature 377:632-635, 1995; Xiang, Z. Q., et al., “Immune responses to nucleic acid vaccines to rabies virus,” Virology 209:569-579, 1995. By “effective amount” of a gene vaccine, we mean an amount of vaccine effective to moderate or eliminate Pseudomonas infection or Pseudomonas infection symptoms.

The protein or antigen could also be used diagnostically to detect antibodies in patients and, thus, predict the patient's infection status. One would preferably contact a sample obtained from an individual suspected of Pseudomonas infection with the PcrV protein or fragment thereof and detect protein/antibody binding. One would then correlate enhanced antibody binding (as compared with a control sample) with Pseudomonas aeruginosa infection in the individual. One could also use the PcrV antibody or antibody fragments therapeutically.

In another embodiment, the invention is the use of the antibody sequence (which we report below and in SEQ ID NOs:1-4) to produce recombinant single chain antibodies that may block PcrV and could also utilize the sequence in gene delivery experiments, where one would deliver eukaryotic vectors that will then lead to the production of single chain antibodies in animals for prolonged periods. The sequence could also be utilized to humanize the murine monoclonal antibody to produce a product that can be utilized in human patient care.

Once the antibody is safe for human use, one could: (a) administer it systemically and (b) administer it into the lungs as either a preventative treatment or as a therapy. In order to use the PcrV antibody in humans, the antibody is preferably “humanized”. In general, once the monoclonal antibody is obtained the heavy and light chain variable regions are cloned. These cloned fragments are then inserted into a human antibody backbone (constant regions). Thus, we can control the class of antibody (IgG, IgA, etc.) in addition to providing the binding specificity.

For use in the present invention, the PcrV antibody may be a monoclonal antibody or polyclonal. The antibodies may be human or humanized, particularly for therapeutic applications. Antibody fragments or derivatives, such as an Fab, F(ab′)₂ or Fv, may also be used. Single-chain antibodies, for example as described in Huston, et al. (Int. Rev. Immunol. 10:195-217, 1993) may also find use in the methods described herein. By “effective amount” of the PcrV antibody or antibody fragment we mean an amount sufficient to moderate or eliminate Pseudomonas infection or infection symptoms.

Preferably, human or humanized monoclonal or polyclonal antibodies to PcrV are administered to prevent or treat infections with P. aeruginosa. In patients at high risk for P. aeruginosa infection, antibodies could be administered for prevention of infection. In addition, antibodies may be administered after the onset of infection to treat the infection. In this case, antibodies can be administered alone or in combination with antibiotics. Administration of antibodies in conjunction with antibiotics may allow the administration of shorter courses or lower doses of antibiotics, thereby decreasing the risk of emergence of antibiotic-resistant organisms.

We envision at least three types of hypothetical patients: (1) A healthy individual at risk of serious injury or burn (fire fighter, military personnel, police) would be immunized with the vaccine by a methodology (either injection or intranasal) that would give long-lived protection. A booster would be given on admission (intramuscular injection) to the hospital after injury. (2) A patient who is being subjected to mechanical ventilation. (3) A patient who has been genetically diagnosed with cystic fibrosis.

In addition to PcrV antibodies and antibody fragments, small molecule peptidomimetics or non-peptide mimetics can be designed to mimic the action of the PcrV antibodies in inhibiting or modulating Pseudomonas infection, presumably by interfering with the action of PcrV. Methods for designing such small molecule mimics are well known (see, for example, Ripka and Rich, Curr. Opin. Chem. Biol. 2:441-452, 1998; Huang, et al., Biopolymers 43:367-382, 1997; al-Obeidi, et al., Mol. Biotechnol. 9:205-223, 1998). Small molecule inhibitors that are designed based on the PcrV antibody may be screened for the ability to interfere with the PcrV-PcrV antibody binding interaction. Candidate small molecules exhibiting activity in such an assay may be optimized by methods that are well known in the art, including for example, in vitro screening assays, and further refined in in vivo assays for inhibition or modulation of Pseudomonas infection by any of the methods described herein or as are well known in the art. Such small molecule inhibitors of PcrV action should be useful in the present method for inhibiting or modulating a Pseudomonas infection.

In another aspect of the present invention, PcrV protein may be used to identify a PcrV receptor which may be present in the host cells, particularly in human cells, more particularly in human epithelial cells or macrophages. Identification of a PcrV receptor allows for the screening of small molecule libraries, for example combinatorial libraries, for candidates that interfere with PcrV binding. Such molecules may also be useful in a method to inhibit or modulate a Pseudomonas infection.

Our first attempts at receptor identification will be to use PcrV in pull-down experiments. PcrV will be fused to glutathione S-transferase (GST) and attached to column matrix for affinity chromatography of solubilized cellular extracts. Proteins binding specifically to PcrV will be eluted and subjected to amino terminal sequencing for identification. In parallel experiments PcrV will be subjected to yeast two-hybrid analysis. In this case PcrV is fused in frame with the DNA binding domain of Gal4. Once the clone is obtained it will be transformed into a suitable yeast host strain. The yeast strain containing the Gal4PcrV construct will be transformed with a Hela cell cDNA bank cloned in frame with the Gal4 activation domain. Double transformants that complement the ability to utilize histidine and produce beta galactosidase (proteins that interact with PcrV) will be analyzed genetically and at the nucleotide sequence level. In case the receptor is a cellular glycolipid we will utilize an overlay technique where glycolipids are separated by thin-layer chromatography and then probed with radiolabeled bacteria. The binding to specific components will be monitored by autoradiography. Similarly, epithelial and macrophage proteins will be separated by SDS-PAGE, blotted onto nitrocellulose and overlaid with radiolabeled bacteria or labeled PcrV. Again, the protein components to which the bacteria bind are then identified by autoradiography.

Pseudomonas species are known to infect a wide spectrum of hosts within the animal kingdom and even within the plant kingdom. As will be apparent to one of ordinary skill in the art, the compositions and methods disclosed herein may have use across a wide range of organisms in inhibiting or modulating diseases or conditions resulting from infection by a Pseudomonas species. The compositions and methods of the present invention are described herein particularly for application to Pseudomonas aeruginosa but it is well within the competence of one of ordinary skill in the art to apply the methods taught herein to other species.

EXAMPLES

1. Role of PcrV in Cytotoxicity

To determine the role of PcrV in type III-mediated regulation/secretion, we constructed a nonpolar allele of PcrV and used the construct to replace the wild-type allele in P. aeruginosa strain PA103, a strain that is highly cytotoxic in vitro (3) and causes lung epithelial damage in vivo (12, 13). Cytotoxicity and lung injury are due to the production of a specific cytotoxin, ExoU (3).

PA103ΔpcrV was characterized by the expression of several extracellular products that are secreted by the P. aeruginosa type III system which include the ExoU cytotoxin (3), PcrV (5), and a protein required for the translocation of toxins, PopD (14). SDS-polyacrylamide gel electrophoresis of concentrated culture supernatants indicated that the parental strain, PA103 is induced for production and secretion of the type III proteins by growth in medium containing a chelator of calcium, nitrilotriacetic acid (NTA) (FIG. 1). When an expression clone encoding PcrV was provided in trans in the parental strain, extracellular protein production in response to the presence or absence of NTA is normal. PA103ΔpcrV exhibits a calcium blind phenotype; extracellular protein production is strongly induced in both the presence and absence of NTA. These results suggest that the secretory system is fully functional but deregulated. This deregulated phenotype is in contrast to the calcium independent phenotype reported for an LcrV defective strain which fails to produce the extracellular Yops, grows at 37° C. regardless of the presence or absence of calcium, and shows only partial induction of the Yops (7). Complementing PA103ΔpcrV with a clone expressing wild-type PcrV restored normal regulation of extracellular protein production in response to NTA induction.

To test the contribution of PcrV to P. aeruginosa pathogenesis, two infection models were used. In an in vitro model the parental and several mutant derivative strains were compared for their ability to cause cytotoxicity in a CHO cell infection assay (3). The negative controls in this experiment included PA103popD::Ω, which has been previously shown to be defective in the translocation of type III virulence determinants (14) and PA103ΔexoU, which is non-cytotoxic due to the absence of ExoU production (3, 15).

After a 3 hour infection, CHO cells were unable to exclude trypan blue with the wild-type and ΔpcrV strain complemented with a plasmid construct expressing PcrV. Staining did not occur when CHO cells were infected with the negative control strains or with PA103ΔpcrV (data not shown). These results suggest that PcrV expression is required for cytotoxicity. Purified recombinant PcrV was not cytotoxic when added exogenously to tissue culture cells. Since secretion of the type III proteins required for translocation was unaffected by the deletion of pcrv (FIGS. 1A and B), PA103ΔpcrV appears to be defective in ExoU translocation.

FIGS. 1A and 1B are a stained gel (FIG. 1A) and Western blot (FIG. 1B) illustrating the phenotypic analysis of PA103ΔpcrV. The parental and ΔpcrV derivatives, with and without a plasmid expressing PcrV in trans, were grown in the absence or presence of the inducer of type III secretion in P. aeruginosa, nitrilotriacetic acid (NTA). The extracellular protein profile (FIG. 1A) was analyzed on a SDS-polyacrylamide gel (10%) stained with Coomassie blue. The migration of the P. aeruginosa-encoded type III proteins is indicated to the left and the migration of molecular weight markers is indicated on the right. FIG. 1B is a Western blot of a duplicate gel using antibodies specific for ExoU, PcrV, and PopD and ¹²⁵I-Protein A to detect bound IgG.

Wild-type and mutant P. aeruginosa strains were tested in an acute lung infection model using low and high challenge doses of bacteria. Survival measurements indicated that PcrV and PopD were required to induce a lethal infection (FIG. 2A). In experiments utilizing three independent measurements of lung injury (the flux of labeled albumin from the airspaces of the lung to the bloodstream, the flux of labeled albumin from the airspaces of the lung to the pleural fluids, and the wet/dry ratio, which measures lung edema) the degree of injury caused by PA103ΔpcrV, the vector control strain (PA103 PA103ΔpcrV pUCP18), and PA103popD::Ω were no different than the uninfected control animals (FIG. 2B). Complementation of PA103ΔpcrV with pcrV in trans restored lung injury levels to those measured with the parental strain, PA103. Taken together these data indicate that PcrV expression is required for virulence of P. aeruginosa in the acute lung infection model and that part of the function of PcrV appears to be linked to the ability to translocate type III effector proteins into eukaryotic cells.

FIGS. 2A and 2B are a graph (FIG. 2A) and set of bar graphs (FIG. 2B) illustrating the survival and lung injury of P. aeruginosa parental and mutant strains. Referring to FIG. 2A, mice were challenged with 5×10⁵ cfu of each of the indicated strains and survival was monitored for one week. Referring to FIG. 2B, lung injury was assessed by the flux of labeled albumin from the airspaces of the lung to the blood (lung epithelial injury), to the pleural fluid (pleural fluid) or by measuring the wet/dry ratio (lung edema). Two bacterial infectious doses were used as denoted by the solid and striped bars. Significant differences (*p<0.001) between control and test groups was determined by one-way ANOVA and Dunnet multiple comparison tests. The following abbreviations were used: PA103, parental wild-type strain; ΔpcrV, PA103ΔpcrV; ΔpcrVpUCPpcrV, PA103ΔpcrV complemented with a plasmid expressing PcrV; ΔpcrVpUCP, PA103ΔpcrV with a vector control; popD::Ω, PA103popD::Ω, a translocation defective strain.

2. Immunization with PcrV

To determine whether immunization with PcrV protected animals from a lethal lung infection, recombinant PcrV (rPcrV) or ExoU (rExoU) were purified as histidine-tagged fusion proteins and used as antigens. Mice were immunized and subsequently challenged via their airspaces with a lethal dose of strain PA103. When survival was measured, both vaccines protected the mice (FIG. 3A). When lung injury was assessed, only PcrV vaccinated animals had significantly less epithelial damage and lung edema (FIG. 3B). Animals immunized with the PcrV vaccine also had significantly fewer bacteria in their lungs, suggesting that a blockade of the Pseudomonas V antigen may facilitate rapid clearance of bacteria from the lung, protecting the animals from severe epithelial injury (FIG. 3B).

FIGS. 3A and 3B are a graph (FIG. 3A) and a set of bar graphs (FIG. 3B) illustrating the effect of immunization on survival, lung injury, and bacterial colonization. Referring to FIG. 3A, mice were immunized (PcrV, n=10; ExoU, n=5; control, n=10) as indicated and challenged with strain PA103 at 5×10⁵ CFU/animal. The percent of surviving animals was determined for one week; p<0.05 by the Mantel-Cox log rank test. Referring to FIG. 3B, lung injury assessment and bacterial colonization of vaccinated animals 4 hours after installation of PA103. Lung epithelial injury, lung edema, and bacterial burden; PcrV, n=9; ExoU, n=4; and control, n=8. The final number of bacteria in the lung is indicated as the number on the Y axis×10⁴ CFU. Significant differences (*) for lung injury (p<0.01), lung edema (p<0.05), and bacterial numbers (p<0.05) as determined by Dunnet multiple comparison test. One-way ANOVA for lung injury, p=0.0005; lung edema, p=0.0437; bacterial burden, p=0.0075.

To determine whether therapeutic intervention was possible, mice were passively immunized with preimmune rabbit IgG or rabbit IgG specific for rPcrV, rExoU, or rPopD one hour prior to airspace instillation of PA103 at a concentration of 5×10⁵ CFU/mouse. Antibodies to rPcrV provided complete protection to a lethal infection (FIG. 4). Anti-rExoU IgG provided partial survival, which was significantly different from the administration of control IgG, although all the surviving animals appeared severely ill during the trial. Survival was not improved by the passive transfer of antibodies to another of the type III translocation proteins, PopD. From these results we conclude that antibodies to PcrV are highly protective in the acute lung infection model and that PcrV may be exposed on the bacterial surface or in a soluble form that is available for antibody-antigen interactions.

FIG. 4 is a graph of the number of animals surviving a challenge with 5×10⁵ CFU/mouse of strain PA103. Animals were pretreated with 100 ug of immune IgG or control IgG from an unimmunized rabbit (rPcrV, preimmune serum). N=10 for each group; *p<0.05 versus control group for treatment with anti-PcrV and anti-ExoU IgG preparations by Mantel-Cox log rank test.

If PcrV is accessible for neutralization, then concomitant administration of the bacterial inoculum with anti-rPcrV IgG should completely protect against lung injury and lethality. IgG preparations were mixed with the inoculum (10-fold higher dose than the lethal inoculum) prior to instillation of the bacteria into the lung and survival was measured. Only anti-rPcrV IgG was protective against this extreme infection (FIG. 5A). Lung injury was measured in animals infected with the normal lethal dose of 5×10⁵ bacteria. The efflux of labeled albumin from the airspaces of the lung was only 3% more than uninfected controls (FIG. 5B) after co-administration of anti-rPcrV IgG. The decreased efflux of labeled protein from the lung to the pleural fluids was the same as the uninfected controls when anti-PcrV was included with the inoculum. Curiously lung edema, as measured by the wet/dry ratio, was significantly reduced by the addition of either anti-rPcrV or anti-rPopD. (FIG. 5B). Thus, the concomitant administration of anti-rPcrV IgG with the bacteria was even more effective in normalizing all the lung injury parameters than vaccination. These data support the accessibility of PcrV for antibody-mediated neutralization and document a clinically relevant decrease in lung injury; antibodies to PcrV may serve as therapeutic reagents in the treatment of severe nosocomial pneumonia caused by Pseudomonas aeruginosa.

FIG. 5 is a graph (FIG. 5A) and a set of bar graphs (FIG. 5B) illustrating survival and protection from lung injury by concomitant administration of IgG and bacterial challenge. IgG (5 ug) was mixed with either 5×10⁶ (for survival assays, n=10 per group) or 5×10⁵ (for the measurement of lung injury, n=4 to 6 animals per group) P. aeruginosa strain PA103. This mixture was instilled into the lungs and survival (FIG. 5A) or lung injury (FIG. 5B) was assessed. For survival, *p<0.05 versus control IgG for anti-PcrV by the Mantel-Cox log rank test; for lung epithelial injury and lung edema *p<0.05 versus control IgG by Dunnet multiple comparison test. One-way ANOVA for lung injury, p=0.026, and lung edema, p<0.0005.

In acute P. aeruginosa infections, the net effect of type III-mediated intoxication may be to promote the dissemination of the bacterium beyond the epithelium leading to infection of the pleural fluids, spleen, liver, and bloodstream. Blood-borne infections with P. aeruginosa from either acute ventilator-associated pneumonia or from burn wound infections can result in a 40-80% mortality rate in spite of aggressive antibiotic treatment (16). PcrV must be a component of the type III translocation complex in P. aeruginosa, as mutants defective in the production of this protein are unable to intoxicate CHO cells or cause lung epithelial injury even though they are able to produce and secrete the type III effectors and proteins required for translocation. Unlike PopD, which is also necessary for translocation, PcrV is accessible for antibody-mediated neutralization suggesting that antibodies may be useful therapeutic agents in acute infections.

3. Methods for Examples 1 and 2

Construction of a nonpolar insertion in PcrV and complementation. A 5.0-kb EcoRI-NsiI restriction fragment encoding pcrGVHpopBD and flanking sequences was cloned into the allelic replacement vector pNOT19 (17). Two NotI sites (one within pcrG and one within popB) were removed from the inserted sequences by using the Sculptor mutagenesis system (Amersham).

An internal SstI restriction fragment was deleted from pcrV, resulting in an in-frame deletion of residues 17-221 (pNOTΔpcrV). To select for integration of the plasmid, a gene encoding tetracycline resistance (TcΩ) was cloned into the HindIII site of the vector (pNOTΩΔpcrV). The MOB cassette (17) was added as a NotI fragment. Selection of merodiploids, resolution of plasmid sequences, and confirmation of allelic replacement was performed as previously described (18). A shuttle plasmid (pUCP, 19) was used to construct a clone to complement the pcrV deletion. The coding sequence for PcrV was amplified and cloned behind the control of the ExoS promoter region (20). The transcription of ExoS is coordinately regulated with the operons that control type III secretion and translocation in P. aeruginosa (2). The nucleotide sequence was confirmed for each DNA construct involving site specific mutagenesis, PCR amplification, or in-frame deletion.

SDS-PAGE and Western blot analysis of secreted products. P. aeruginosa were grown under inducing (+NTA) or non-inducing conditions (−NTA) for expression of the type III secreted products (18). Cultures were harvested based on optical density measurements at 540 nm and supernatant fractions were concentrated by the addition of a saturated solution of ammonium sulfate to a final concentration of 55%. Each lane of an SDS-polyacrylamide gel (11%) was loaded with 3 pi of a 20-fold concentrated supernatant and stained with Coomassie blue. An identical gel was subjected to Western blot analysis as previously described (3-5) using a cocktail of rabbit antisera, which specifically recognizes ExoU, PopD, and PcrV. Protein A labeled with ¹²⁵I was used as a secondary reagent to identify bound IgG.

Infection models and lung injury assessments. Chinese Hamster Ovary cells (CHO) were used in an in vitro infection model designed to measure cytotoxicity and type III translocation (21). Briefly, a bacterial inoculum was prepared in tissue culture medium without serum. CHO cells, which were propagated in serum containing medium, were washed and infected with various P. aeruginosa strains at a multiplicity of infection of 5:1. Cultures were incubated under tissue culture conditions for 3 hours (37° C., 5% CO₂), washed, and stained with trypan blue. Permeability to the dye was determined from phase contrast photographs. Infection with the parental strain PA103, which expresses ExoU, results in trypan blue staining of approximately 80% of the monolayer after 3 hours of incubation and complete destruction of the monolayer at 4-5 hours of incubation. Mouse infections and assessment of lung injury was performed as previously described (16). Briefly, male 8- to 12-week old pathogen-free BALB/c mice were purchased from Simonsen Laboratories (Gilroy, Calif.) and housed in barrier conditions. The mice were briefly anesthetized with inhaled Metofane (methoxyflurane, Pitman-Moore, Mundelein, Ill.) and placed supine, at an angle of approximately 30°. Fifty microliters of the bacterial inoculum was instilled slowly into the left lobe using a modified 24 gauge animal feeding needle (Popper & Sons, Inc., New Hyde Park, N.Y.) inserted into the trachea via the oropharynx. When lung injury assessments were measured, 0.5 μCi of ¹³¹I-labeled human serum albumin (Merck-Frosst, Quebec, Canada), 0.05 μg of anhydrous Evans blue in ml of Ringer's lactate with 5% mouse albumin were added to the instillate. After 4 hours of infection, the mice were anesthetized, blood was collected by a carotid arterial puncture and median sternotomies were performed. The lungs, pleural fluids, tracheas, oropharynxes, stomachs, and livers were harvested, and the radioactivity was measured. The percentage of radioactive albumin that left the instilled lungs and entered the circulation or the pleural fluid was calculated by multiplying the counts measured in the terminal blood samples (per ml) times the blood volume (body weight×0.07). The wet-dry ratios of the lungs were determined by adding 1 ml of water to the lungs and homogenizing the mixture. Homogenates were placed in preweighed aluminum pans and dried to constant weight in an 80° C. oven for three days. Lung homogenates were also sequentially diluted and plated on sheep blood agar for quantitative assessment of bacteria.

Production of rabbit antiserum to PcrV, PopD, and ExoU. rPcrV, rPopD, and rExoU were produced as histidine tagged fusion proteins in pET16b and purified by nickel chromatography as previously described (22). Rabbits were injected intradermally (10 sites) with 300 μg of recombinant protein emulsified in Freund's complete adjuvant, boosted with antigen in Freund's incomplete adjuvant, and periodically bled at 7 day intervals. For passive immunization, the IgG fraction was isolated using Protein A column chromatography (Pierce Chemicals, Rockford, Ill.). Mice were injected with 100 μg IgG (intraperitoneal injection) 1 hour before challenge with 5×10⁵ CFU of strain PA103. For active immunization with rPcrV and rExoU, endotoxin was removed from protein preparations by extraction with 1% Triton X-114 (23). Following the extractions, Triton X-114 was removed by Sephacryl S-200 chromatography. All vaccine preparations contained less than 1 ng of endotoxin per 40 μg of recombinant protein as determined by using a limulus amebocyte lysate assay (BioWhittaker, Walkersville, Md.). BALB/c mice were injected subcutaneously with 10 μg of recombinant proteins in Freund's complete adjuvant. At day 30 the mice were boosted with an additional 10 μg of antigen in Freund's incomplete adjuvant. On day 51 the mice were challenged by instillation of P. aeruginosa into their left lungs.

4. Synthesis of Monoclonal Antibodies

Mice were immunized with 10 μg of purified, LPS-free, recombinant PcrV in Freund's complete adjuvant and boosted two weeks later with the same dose of antigen emulsified in Freund's incomplete adjuvant. Immunizations were performed subcutaneous Spleens were harvested from mice one week after booster doses of PcrV in Freund's incomplete adjuvant.

A single spleen was placed in 5 ml of tissue culture medium without serum, cut into pieces and gently homogenized. Large pieces of tissue were allowed to settle from the homogenate and the supernatant, single-cell suspension was removed and subjected to centrifugation at 1200 rpm for 10 minutes. The pelleted cells were resuspended in 10 ml of a solution to lyse red blood cells for 5 minutes and subsequently underlaid with 10 ml of fetal bovine serum. The material was centrifuged at 1200 rpm for 8 minutes, the supernatant was discarded and the cells were suspended in 30 ml of medium.

Spleenic cells and myeloma cells (P3x63Ag8.653) were harvested by centrifugation at 1200 rpm for 10 minutes, and each pellet was separately suspended in 10 ml of tissue culture medium. 10⁸ spleen cells and 2×10⁷ myeloma cells were mixed and pelleted together by centrifugation at 1200 rpm for 6 minutes. The supernatant was removed by aspiration and 1 ml of 35% polyethylene glycol (PEG) was added. The cells were suspended in this solution gently and centrifuged at 1000 rpm for 3 minutes. In some experiments centrifugation was eliminated.

Exactly 8 minutes after the addition of PEG, 25 ml of medium was added and the cells were gently resuspended. Following a 5 minute 1200 rpm centrifugation step, the cell pellet was suspended at a density of 1×10⁶ per ml in 30% conditioned medium and 70% complete medium (with serum). The cells were incubated overnight at 37° C. The next day the cells were harvested by centrifugation and suspended in 200 ml of 30% conditioned medium and 70% complete medium with hypoxanthine, aminopterin and thymidine (HAT).

Approximately 0.2 ml of this cell suspension was added per well to ten 96-well plates (12 ml per 96 well plate). The density of the remaining cells was adjusted to 2.5×10⁵ per ml and the cells were plated in the 96 well format. Plates were screened microscopically for single colonies and supernatants were subsequently tested for antibody production by enzyme-linked immunosorbent assay using recombinant PcrV as the antigen. Clones producing antibodies reactive to PcrV were subcultured to larger culture dishes and then isotyped.

The binding of antibodies was tested in an enzyme linked immunosorbent assay using recombinant PcrV as the antigen (histidine-tagged protein) coating the wells. Monoclonal antibodies were also tested in Western blot reactions using a P. aeruginosa supernatant containing native PcrV without the histidine tag.

5. Identification of PcrV Antigen

We obtained about three hundred cell lines producing antibodies that bound the tagged PcrV. These initial cell lines were preserved in liquid nitrogen for safekeeping. All cell lines were passaged to isolate stable clones. In conjunction with isolating stable clones we developed in in vitro assay as a correlate for protection against intoxication in animal infection models.

The hybridomas that were stable to passage and still produced antibodies reactive to PcrV in ELISA (approximately 80 cell lines) were subsequently tested in a Fluorescence Activated Cell Sorter using the following techniques and assumptions: We reasoned that if antibody is blocking the type III intoxication system, then in the presence of a monoclonal that blocks, fewer cells will be killed by our toxins. We exposed cells to each of the 80 monoclonal antibodies, added toxic bacteria, incubated, and then added a dye that is only permeable to dead cell DNA (propidium iodide). Excess dye was washed away and the cells were harvested, fixed, and analyzed by FACS. Dead cells would be fluorescent since the dye leaked in and stained DNA in the nucleus.

We found that if the cells were incubated with rabbit polyclonal anti-PcrV, mouse polyclonal anti-PcrV, or mab166 and bacteria, fewer cells died than in controls with irrelevant polyclonal antibody (anti-PopD) or the other 78 monoclonal antibodies.

Mab 166 was specifically found to bind to the bacterially encoded type III-secreted factor termed PcrV. PcrV mediates the interaction of P. aeruginosa and lung cells to facilitate the translocation of bacterial toxins that cause cellular death. This reaction is postulated to eliminate lung cells that are involved in the innate immune response to P. aeruginosa. The killing of these cells leaves the host epithelium open for P. aeruginosa colonization and spread to the pleural fluids and bloodstream. P. aeruginosa-encoded antibiotic resistance makes effective treatment unlikely once the bacteria have entered the bloodstream.

The protection afforded by mab 166 pre- and post-bacterial instillation in animal models of acute lung infection with P. aeruginosa is significant. To design antibody treatment modalities for intervention in human P. aeruginosa infections it will be necessary to produce either a human monoclonal antibody or to immunize at risk patients with the protective epitope of PcrV defined by mab 166. The goal of the work described below is to define the amino acid sequence of PcrV bound by mab 166.

Results

We used a molecular genetic approach to define the amino acid residues bound by mab 166. PcrV possesses 294 amino acids. The approach consisted of deleting parts of the molecule at the nucleotide sequence level using the polymerase chain reaction. Each product was cloned into a protein expression vector in frame with a gene encoding the glutathione S transferase protein. This strategy ensured that deletions encoding small numbers of PcrV amino acids could be detected using Western or dot blot techniques. Control bacterial lysates encoding only glutathione S transferase showed no reactivity to either our anti-PcrV polyclonal or mab 166 monoclonal antibody.

A total of 66 (with one full-length PcrV expression plasmid) clones were constructed, expressed, and tested for reactivity to rabbit polyclonal anti-PcrV antisera. All but one clone bound to anti-PcrV rabbit antibody verifying that the expressed proteins were in-frame with PcrV. The one non-reactive clone was eliminated from the analysis. None of the C-terminal deletions (n=5 constructs) bound mab 166 suggesting that the epitope was in the C-terminal half of the protein. Only one of the N-terminal truncation proteins (n=8 constructs) encoding PcrV amino acids (aa) 139-294 bound to mab 166. This experiment verified our hypothesis that the mab 166 epitope was encoded by the carboxyl terminal half of the protein. The remaining 51 constructs encoded various internal deletions of the molecule. Binding analysis tabulated in Table 1, below, demonstrated that the smallest epitope recognized by mab 166 consists of aa 144-257 of PcrV.

TABLE 1 PcrV Epitope Mapping All proteins are amino-terminal tagged GST-PcrV truncates Amino Acids Binding to pAb Binding to mAb 166 1-294 (full-length) Yes Yes (C-term truncates)  1-46 yes no  1-76 yes no  1-134 yes no  1-172 yes no 1-75 + 173-294 yes no (N-term truncates) 139-294 yes yes 148-294 yes no 159-294 yes no 164-294 yes no 194-294 yes no 261-294 yes no 269-294 yes no 278-294 yes no (internal fragments) 139-191 yes no 139-195 yes no 139-234 yes no 139-243 yes no 139-256 yes no 139-257 yes yes; weak 139-258 yes yes 139-259 yes yes 139-260 yes yes 139-261 yes yes 139-262 yes yes 139-263 yes yes 139-264 yes yes 139-265 yes yes 139-266 yes yes 139-274 yes yes 139-281 yes yes 140-266 yes yes 141-266 yes yes 142-266 yes yes 143-266 yes yes 144-266 yes yes 145-266 yes no 146-266 yes no 147-266 yes no 148-170 no* no 148-202 yes no 159-202 yes no 159-209 yes no 159-216 yes no 159-226 yes no 159-234 yes no 164-234 yes no 164-243 yes no 164-256 yes no 164-266 yes no 164-275 yes no 164-281 yes no 194-234 yes no 194-243 yes no 194-256 yes no 194-266 yes no 194-275 yes no 194-281 yes no 141-258 yes yes; weak 142-258 NT** yes 143-258 yes yes 144-258 yes yes 141-257 yes yes 142-257 yes yes 143-257 yes yes 144-257 yes; weak yes; weak Notes: *Truncate 148-170 is the only one that is not recognized by the rabbit polyclonal control antibody. **NT: Not tested due to an insufficient amount of bacterial lysate. As predicted, pGEX-4T-2 vector control lysates were not recognized by either antibody. The smallest epitope of PcrV recognizable by mAb166 appears to consist of amino acids 144-257.

6. Examination of PcrV-Specific Antibody

Methods:

Poly A+ RNA extraction: Hybridoma cell line ml 66 was cultured in complete Dulbeccos minimum essential medium with 4.5 g/L D-glucose, 10 mM HEPES, 50 μM 2-mercaptoethanol, 3 mM L-glutamine, and 10% heat-inactivated fetal calf serum, 100 U/mL penicillin and 100 μg/mL streptomycin sulfate. After the cells reached confluent state in a 75 cm² flask, the cells were harvested from centrifuging at 600 rpm for 5 minutes. The pellet of the cells was homogenized in 2 mL of TRIzol reagent (Life Technologies, Gaithersburg, Md.), and total RNA (100 pg) was extracted after chloroform fractionation, isopropanol precipitation and 70% ethanol wash. Poly A+ RNA (4 μg) was extracted with oligotex mRNA spin-column (Qiagen, Valencia, Calif.).

RNA oligo-capping: mRNA (250 ng) was incubated with calf intestinal phosphatase at 50° C. for 1 hour to dephosphorylate non-mRNA or truncated mRNA. After the reaction, phenol/chloroform extraction and ethanol precipitation was performed and the dephosphorylated RNA was incubated with tobacco acid pyrophosphatase at 37° C. for 1 hour to remove the 5′-cap structure from full-length mRNA. After phenol/chloroform extractions and ethanol precipitation, the synthetic RNA oligo (GeneRacer RNA Oligo, Invitrogen, Carlsbad, Calif.) was ligated to the decapped RNA with T4 RNA ligase at 37° C. for 1 hour. After phenol/chloroform extraction and ethanol precipitation, the RNA was suspended in 13 μL diethylpyrocarbonate-treated water.

Reverse-transcribing mRNA: The RNA-oligo ligated, full-length mRNA (13 μL) was reverse-transcribed with 54 base the pair primer containing a dT tail of 18 nucleotides (GeneRacer Oligo dT, Invitrogen), and Avian myeloblastosis virus reverse transcriptase at 42° C. for 1 hour in 20 μL reaction. After the reaction, the sample was diluted 4 times with sterile water.

Amplifying cDNA ends by polymerase chain reaction (PCR): One microliter of the cDNA was used for PCR. The 5′ primer from the synthetic RNA oligo sequence (GeneRacer 5′ Primer, Invitrogen) and the murine immunoglobulin gamma 2b chain CH1 region specific primer or the murine immunoglobulin kappa chain CL region specific primer were used. The cycling parameters used for the PCR reaction was; 1) 94° C., 2 minutes, 1 cycle, 2) 94° C., 30 seconds and 72° C., 1 minute, 5 cycle, 3) 94° C., 30 seconds, 70° C., 30 seconds, and 72° C., 1 minutes, 5 cycle, 4) 94° C., 30 seconds, 68° C., 30 seconds, and 72° C., 1 minutes, 20 cycle, 5) 72° C., 10 minutes.

Subcloning and DNA sequencing: PCR products (the murine immunoglobulin gamma 2b chain CH1 region derived fragment and the murine immunoglobulin kappa chain CL region derived fragment) were subcloned into the PCRII vector (TOPO cloning, Invitrogen) and submitted to UCSF Molecular Bioresource Center to analyze the DNA sequence.

SEQ ID NO:1 is the DNA sequence of m166 heavy chain mRNA, SEQ ID NO:2 is the amino acid sequence of the m166 heavy chain (IgG II^(b)), SEQ ID NO:3 is the DNA sequence of the ml 66 light chain mRNA, and SEQ ID NO:4 is the amino acid sequence of the m166 light chain. FIGS. 6A, 6B and 7 examine the sequences and supply more detail.

Commercial Implications

One could use the antibody sequence to produce recombinant single chain antibodies that may block PcrV and could also utilize the sequence in gene delivery experiments, where one would deliver eukaryotic vectors that will then lead to the production of single chain antibodies in animals for prolonged periods. Finally, the sequence could be utilized to humanize the murine monoclonal antibody to produce a product that can be utilized in human patient care. One of skill in the art would look to standard methods such as grafting the antigen binding complementarity determining regions (CDRs) from variable domains of rodent antibodies on to human variable domains in order to create a humanized antibody.

7. Single Chain Antibody Against PcrV

a. Assembling a Single Chain Antibody:

VH gene and VL gene were multiplied by polymerase chain reaction (PCR) with specific primers for each gene. Multiplied VH and VL fragments were assembled with a linker by using PCR with primers. The assembled single chain antibody gene (scFv::m166:VH and VL genes with linker) was transferred into the cloning vector pCR4 Topo (Invitrogen, Carlsbad, Calif.). Then, the coding sequence of scFv::m166 was subcloned into the E. coli expression vector pBAD/gIII (Invitrogen) in LMG194 as the host E. coli.

b. Protein Induction and Purification:

For protein induction, in RM medium containing 0.2% glucose and 100 μg of ampicillin, the transformed E. coli was cultured overnight at 37° C. in an orbital shaker (200 rpm), and the next day, 5 mL of the cultured E. coli was transferred into 500 mL of the same medium and incubated for 3 hours at room temperature at 100 rpm. After L-arabinose was added at the concentration of 0.004%, the E. coli was cultured overnight. The third day, the protein was harvested from the periplasmic space of the E. coli by osmotic shock methods. The solution including osmotic shock derived periplasmic protein was dialyzed overnight against the lysis buffer. During the fourth day, the dialyzed solution was applied onto a nickel-NTA column to purify the hexahistidine-tagged single chain antibody. The eluted solution from the nickel column was dialyzed against phosphate buffered saline overnight. On the fifth day, the dialyzed solution was applied to a centrifuge concentrator to make a higher concentration of scFv:m166.

c. The Binding Test:

The purified single chain antibody (scF::m166) was tested by using an enzyme linked immunosorbent assay against recombinant PcrV and by immunoblot (western blot) against both recombinant PcrV protein and native PcrV of P. aeruginosa PA103.

The single chain antibody will allow us to humanize the antibody utilizing phage-display techniques and to improve affinity of the antibody using these techniques. The single chain antibody can be utilized as a diagnostic tool (for histology) but would not be utilized as a therapy. However, the gene for the single chain antibody can be utilized in gene therapy, so that animals would produce single-chain antibodies over an interval, which could lead to protection against P. aeruginosa infections.

8. References

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1. A method of diagnosing Pseudomonas aeruginosa infection comprising: (a) exposing a patient's sample to a nucleotide probe, wherein the probe hybridizes specifically to nucleotides between residues 626-1510 of SEQ ID NO:8 or nucleotides encoding amino acid residues 144-257 of SEQ ID NO: 7, and wherein the probe comprises a single nucleotide sequence consisting of at least forty contiguous nucleotides between residues 626-1510 of SEQ ID NO:8; (b) detecting the hybridization via PCR or RT-PCR with two primers, wherein each primer consists of a single nucleotide sequence consisting of at least 25 continuous nucleotides between residues 626-1510 of SEQ ID NO:8; and (c) correlating Pseudomonas aeruginosa infection with the presence of the hybridized probe.
 2. A method of diagnosing Pseudomonas aeruginosa infection comprising: (a) exposing a patient's sample to a nucleotide probe, wherein the probe hybridizes specifically to nucleotides between residues 626-1510 of SEQ ID NO:8 or nucleotides encoding amino acid residues 144-257 of SEQ ID NO: 7, and wherein the probe comprises a single nucleotide sequence consisting of at least forty contiguous nucleotides between residues 626-1510 of SEQ ID NO:8; (b) detecting the hybridization via PCR or RT-PCR with a PCR primer consisting of a single nucleotide sequence consisting of at least 25 continuous nucleotides between residues 626-1510 of SEQ ID NO:8; and (c) correlating Pseudomonas aeruginosa infection with the presence of the hybridized probe. 